Variant report

Variant	rs334110
Chromosome Location	chr2:179066443-179066444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178977088..178978663-chr2:179064032..179066620,2	K562	blood:
2	chr2:179060830..179065562-chr2:179066300..179070960,4	K562	blood:

Variant related genes	Relation type
ENSG00000155636	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10197166	0.93[JPT][hapmap]
rs10930827	0.81[JPT][hapmap]
rs13403689	0.86[JPT][hapmap]
rs186736	0.93[JPT][hapmap]
rs2366157	0.93[JPT][hapmap];0.84[MKK][hapmap]
rs2366365	0.82[AFR][1000 genomes]
rs333996	0.93[JPT][hapmap]
rs334005	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs334007	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs334017	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs334024	0.81[JPT][hapmap]
rs334028	0.80[JPT][hapmap]
rs334035	0.93[JPT][hapmap]
rs334037	0.80[JPT][hapmap]
rs334040	0.93[JPT][hapmap]
rs334041	0.86[JPT][hapmap]
rs334042	0.93[JPT][hapmap]
rs334043	0.86[JPT][hapmap]
rs334044	0.86[JPT][hapmap]
rs334045	0.93[JPT][hapmap]
rs334092	0.81[AFR][1000 genomes]
rs334102	0.87[ASW][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs334103	0.86[ASW][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs334115	0.83[AFR][1000 genomes]
rs334117	0.81[AFR][1000 genomes]
rs334122	0.85[AFR][1000 genomes]
rs334126	0.82[AFR][1000 genomes]
rs334132	0.80[AFR][1000 genomes]
rs334133	0.82[AFR][1000 genomes]
rs407528	0.81[AFR][1000 genomes]
rs437523	0.82[AFR][1000 genomes]
rs6719178	0.93[JPT][hapmap]
rs73028675	0.81[ASN][1000 genomes]
rs7419749	0.81[JPT][hapmap]
rs7581504	0.92[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7595650	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv875454	chr2:179022751-179066443	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs334110	SCRN3	cis	cerebellum	SCAN
rs334110	UBAP2L	trans	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179060600-179069800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:179060800-179070000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:179060800-179076200	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:179061000-179069200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:179061000-179069800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:179061000-179070000	Weak transcription	Brain Substantia Nigra	brain
7	chr2:179061000-179070800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:179061200-179068800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:179061400-179069800	Weak transcription	HMEC	breast
10	chr2:179061600-179070000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:179062200-179069200	Weak transcription	Fetal Brain Male	brain
12	chr2:179062400-179069400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:179062800-179068800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:179062800-179069600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:179064600-179069600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:179065000-179069000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:179065000-179069400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:179066000-179066600	Enhancers	Psoas Muscle	Psoas
19	chr2:179066400-179066800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:179066400-179067200	Enhancers	K562	blood

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